This is an R Markdown Notebook. When you execute code within the notebook, the results appear beneath the code.

Try executing this chunk by clicking the Run button within the chunk or by placing your cursor inside it and pressing Ctrl+Shift+Enter. # Cellchat

source("./tianfengRwrappers.R")
Registered S3 method overwritten by 'data.table':
  method           from
  print.data.table     
Registered S3 method overwritten by 'htmlwidgets':
  method           from         
  print.htmlwidget tools:rstudio
载入需要的程辑包:dplyr

载入程辑包:‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

载入需要的程辑包:reticulate
载入需要的程辑包:tidyr

载入程辑包:‘MySeuratWrappers’

The following objects are masked from ‘package:Seurat’:

    DimPlot, DoHeatmap, LabelClusters, RidgePlot, VlnPlot


载入程辑包:‘cowplot’

The following object is masked from ‘package:ggpubr’:

    get_legend

载入需要的程辑包:viridisLite

载入程辑包:‘reshape2’

The following object is masked from ‘package:tidyr’:

    smiths

NOTE: Either Arial Narrow or Roboto Condensed fonts are required to use these themes.
      Please use hrbrthemes::import_roboto_condensed() to install Roboto Condensed and
      if Arial Narrow is not on your system, please see https://bit.ly/arialnarrow

Registered S3 method overwritten by 'enrichplot':
  method               from
  fortify.enrichResult DOSE
clusterProfiler v3.14.3  For help: https://guangchuangyu.github.io/software/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
Registering fonts with R

载入程辑包:‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

载入需要的程辑包:Biobase
载入需要的程辑包:BiocGenerics
载入需要的程辑包:parallel

载入程辑包:‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
    parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:dplyr’:

    combine, intersect, setdiff, union

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval,
    evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

载入需要的程辑包:e1071

载入程辑包:‘widgetTools’

The following object is masked from ‘package:dplyr’:

    funs


载入程辑包:‘DynDoc’

The following object is masked from ‘package:BiocGenerics’:

    path


载入程辑包:‘DT’

The following object is masked from ‘package:Seurat’:

    JS
library(CellChat)
载入需要的程辑包:igraph

载入程辑包:‘igraph’

The following object is masked from ‘package:Mfuzz’:

    membership

The following object is masked from ‘package:DynDoc’:

    path

The following objects are masked from ‘package:BiocGenerics’:

    normalize, path, union

The following object is masked from ‘package:plotly’:

    groups

The following object is masked from ‘package:clusterProfiler’:

    simplify

The following object is masked from ‘package:tidyr’:

    crossing

The following objects are masked from ‘package:dplyr’:

    as_data_frame, groups, union

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Registered S3 methods overwritten by 'registry':
  method               from 
  print.registry_field proxy
  print.registry_entry proxy

CellChat

配体-受体+辅因子

df.net
Registered S3 method overwritten by 'cli':
  method     from    
  print.boxx spatstat

cellchat可视化

# pheatmap(mat, display_numbers = FALSE, number_color ="black", cluster_rows = FALSE, 
         # cluster_cols = FALSE, color = colorRampPalette(c("#1E90FF", "white", "#ff2121"))(400), border_color = NA)
table(cor@idents)

       EC1      SMC_3    Mod_SMC Macrophage    T_cell1      SMC_0      SMC_2    T_cell2    T_cell3        EC2 
      4798       1021       1224       9832      12245       3430       1590       4125        366       1294 
    B_cell  Mast_cell      SMC_1 
      2206        430       2294 

mod_SMC – ACKR3

#chord plot
## 免疫细胞 c(4,5,8,9,11) 和SMC c(2,3,6,7,13)的关系
netVisual_chord_gene(cor, sources.use = c(4,5,8,9,11), targets.use = c(2,3,6,7,13), lab.cex = 0.5, legend.pos.y = 30)

##SMC内部
netVisual_chord_gene(cor, sources.use = c(7,13), targets.use = c(2,3,6), lab.cex = 0.5, legend.pos.y = 30)
#指定pathway
pathways.show <- c("TNF") 
# Hierarchy plot
vertex.receiver = c(2,3,6,7,13) # a numeric vector. 
netVisual_aggregate(cor, signaling = pathways.show, layout = "hierarchy", vertex.receiver = vertex.receiver)

netVisual_aggregate(cor, signaling = pathways.show, layout = "circle")

# netVisual_aggregate(cor, signaling = pathways.show, layout = "chord")

# Heatmap
netVisual_heatmap(cor, signaling = pathways.show, color.heatmap = c("#f1f1f1", "#ff2121"))
Do heatmap based on a single object 

#可视化单个配体受体对的影响
netAnalysis_contribution(cor, signaling = pathways.show)

Add a new chunk by clicking the Insert Chunk button on the toolbar or by pressing Ctrl+Alt+I.

When you save the notebook, an HTML file containing the code and output will be saved alongside it (click the Preview button or press Ctrl+Shift+K to preview the HTML file).

The preview shows you a rendered HTML copy of the contents of the editor. Consequently, unlike Knit, Preview does not run any R code chunks. Instead, the output of the chunk when it was last run in the editor is displayed.

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